Sandbox6 Eric Martz

Please do not edit this page. Eric Martz, February 2011.

Homology Model for 83-341

 * Homology model of 83-341 on template chain A of 3e4c, 52% sequence identity (restore initial scene ). Confidence in this model is high because of the 52% sequence identity and sequence alignment with only one 10-residue gap.

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 * Segment 83-140.
 * The distribution of charges seems unremarkable. Bear in mind that sidechain rotamer positions are incorrect in a homology model.
 * The inner face of 95-140 is partially hydrophobic . Bear in mind that sidechain rotamer positions are incorrect in a homology model. Hide 141-341 . The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the corresponding residues 147-205 in the template 3e4c.


 * The inner face of 95-140 is highly conserved, even based upon a multiple sequence alignment that includes mostly types other than 12 Hide 141-341.
 * When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a few on the outside face are highly conserved, namely Asn130, Val135, Val136, Glu139, Asn140. Hide 141-341.


 * The homology model can be downloaded from homology-model-83-341.

Homology Model for 2-88
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 * Swiss-Model produced a homology model for residues 2-88 using chain A of 1dgn as template. Confidence in this model is low because the sequence alignment had only 19% identity.
 * This model shows a noteworthy separation of charges, with a large region containing only negative charges.
 * Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a conserved patch that may be of interest (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
 * Cartoon
 * Cartoon decorated with conserved residues
 * <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling
 * This model can be downloaded from model-2-88.